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Bug #13252

open

[CWL] RunInSingleContainer requirement errors on DockerRequirement even when no such requirement is specified

Added by Jiayong Li almost 7 years ago. Updated almost 2 years ago.

Status:
New
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Story points:
-
Release:
Postponed
Release relationship:
Auto

Description

I'm trying to run a workflow in a single container but it failed. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-8d7o1hq6mnnri85

I've got the following error.

2018-03-21T00:06:23.256283830Z [step eagle] start
2018-03-21T00:06:23.260142930Z Exception on step 'eagle'
2018-03-21T00:06:23.260701530Z Cannot make scatter job: --no-container, but this CommandLineTool has DockerRequirement under 'requirements'.
2018-03-21T00:06:23.261063530Z Workflow cannot make any more progress.
2018-03-21T00:06:23.261720930Z Final process status is permanentFail

However, the script eagle.cwl does NOT have DockerRequirement.

See the attached tar ball for the cwl scripts. The command I was using:

arvados-cwl-runner --api=containers --submit --no-wait --project-uuid su92l-j7d0g-huzwo8ptw745hjx phasing-wf.cwl yml/phasing-GS12877.yml

Note that without the RunInSingleContainer requirement, the workflow completed. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-94180nzfj7yz6q5

For the record

arvados-cwl-runner --version
/usr/bin/arvados-cwl-runner 1.0.20180223182850, arvados-python-client 0.1.20180223161544, cwltool 1.0.20180130110340

Files

Phasing.tar.gz (1.53 KB) Phasing.tar.gz Jiayong Li, 03/21/2018 04:07 PM

Related issues 1 (0 open — 1 closed)

Related to Lightning - Task #13215: Write phasing workflow with eagle v2.4ResolvedJiayong Li03/22/2018

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 #1

Updated by Jiayong Li almost 7 years ago

  • Status changed from New to In Progress
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 #2

Updated by Jiayong Li almost 7 years ago

  • Related to Task #13215: Write phasing workflow with eagle v2.4 added
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 #3

Updated by Jiayong Li almost 7 years ago

  • File Phasing.tar.gz Phasing.tar.gz added
  • Subject changed from RunInSingleContainer requirement errors on DockerRequirement even when no such requirement is specified to [CWL] RunInSingleContainer requirement errors on DockerRequirement even when no such requirement is specified
  • Description updated (diff)
  • Status changed from In Progress to New
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 #4

Updated by Peter Amstutz almost 7 years ago

This is interesting, you're submitting the whole workflow with RunInSingleContainer and not just a subworkflow, I haven't tested that case. The behavior probably needs to be tweaked.

As a workaround, try putting the DockerRequirement under hints instead of requirements.

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 #5

Updated by Jiayong Li almost 7 years ago

As Peter have noted, the run succeeded after moving the docker requirement under hints. https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-tbz5tqgxp1p5x4h

In other words, changing

cwlVersion: v1.0
class: Workflow
$namespaces:
  arv: "http://arvados.org/cwl#" 
requirements:
  arv:RunInSingleContainer: {}
  DockerRequirement:
    dockerPull: l7g-ml/phasing

to
cwlVersion: v1.0
class: Workflow
$namespaces:
  arv: "http://arvados.org/cwl#" 
requirements:
  arv:RunInSingleContainer: {}
hints:
  DockerRequirement:
    dockerPull: l7g-ml/phasing

Still I'd consider this a minor bug worth fixing.

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 #6

Updated by Lucas Di Pentima almost 2 years ago

  • Release set to 60
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